Tag: Comparative Genome Viewer (CGV)

Comparing Yeast Species Used in Beer Brewing and Bread Making

Using the NIH Comparative Genomics Resource (CGR) to gain knowledge about less-researched organisms

The scientific community relies heavily on model organism research to gain knowledge and make discoveries. However, focusing solely on these species misses valuable variation. Comparative genomics allows us to use knowledge from a model species, such as Saccharomyces cerevisiae, to understand traits in other, related organisms, such as Saccharomyces pastorianus or Saccharomyces eubayanus. Applying this information may provide valuable insight for other less-researched organisms. The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help you do just that. Continue reading “Comparing Yeast Species Used in Beer Brewing and Bread Making” →

New Fungal Alignments Available in the Comparative Genome Viewer (CGV)

Recognizing Fungal Disease Awareness Week

Fungal pathogens are a growing threat to global public health. To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as Fungal Disease Awareness Week.

In honor of this week, we’re highlighting whole genome alignments for fungal pathogens that are now available in the Comparative Genome Viewer (CGV) – NCBI’s latest genome visualization tool.  Alignment displays in CGV help you identify rearrangements and differences in genomic structure such as deletions, inversions, and translocations. These differences can be important for understanding genome plasticity, genetic diversity within species (PMC8640552) and the response to environmental stresses such as exposure to anti-fungal drugs (PMC5555451).    Continue reading “New Fungal Alignments Available in the Comparative Genome Viewer (CGV)” →

Which animals can catch and transmit human viral infections?

Using the NIH Comparative Genomics Resource (CGR) to understand susceptibility to SARS-CoV-2 and other infections

Are you conducting research on animal-mediated transmission of human viral infections, such as COVID-19? The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help with comparative genomics analysis for eukaryotic genes, such as Angiotensin-converting enzyme 2 (ACE2) which is targeted by SARS-CoV-2.

NCBI resources have been beneficial in helping the scientific community understand viral infections associated with public health crises, such as COVID-19 and Influenza, and can be used for study of emerging viruses that may represent new threats. Continue reading “Which animals can catch and transmit human viral infections?” →

NCBI at the Biodiversity Genomics Academy 2023 (BGA23)

Virtual Talks, September 14, 2023

NCBI will be presenting virtually at the Biodiversity Genomics Academy 2023 (BGA23) on September 14, 2023. Our short, interactive talks will focus on NCBI Datasets and the Comparative Genome Viewer (CGV). Both resources are part of the NIH Comparative Genomics Resource (CGR), which facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Recordings will be made available post-event! Continue reading “NCBI at the Biodiversity Genomics Academy 2023 (BGA23)” →

Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI

Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded Human Pangenome Research Consortium (HPRC) has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences from the different genomes to one another. The pangenome allows researchers to compare these DNA sequences and get a more detailed view of the range of human genetic variation. This is the first step toward the HPRC’s goal of building a pangenome reference comprised of the genomes of 350 individuals from diverse genetic backgrounds. Continue reading “Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI” →

New! The Comparative Genome Viewer (CGV) Dot Plot

Get a High-Level View of Assembly-Assembly Alignments

New feature! We added an alternate view in the Comparative Genome Viewer (CGV) that shows a dot plot (also known as a 2D plot) comparing two related genome assemblies. This added view provides a high-level overview of the assembly-assembly alignment. Dot plots help you find large genome rearrangements such as translocations or segmental duplications more easily.

Using the Dot Plot View

From the main CGV view, you can access the dot plot by clicking on the new ‘Go to dot plot view’ link.
Click on a cell in the plot to zoom to a pairwise comparison between two chromosomes.
You can return to the main CGV view by clicking on ’Go to ideogram view’.
When you return to the ideogram view from the chromosome level dot plot view, you’ll see the same chromosomes you were looking at in the dot plot. Here, you can zoom further to investigate gene annotation and obtain alignment details.

Continue reading “New! The Comparative Genome Viewer (CGV) Dot Plot” →

Revolutionize your research with the NIH Comparative Genomics Resource (CGR)

Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.  

Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)” →

New NCBI Summer Virtual Workshop Series!

Apply to attend interactive, hands-on workshops

Calling all biology students and educators! Want to learn more about NCBI resources and how to use our high-quality data and cutting-edge tools for your research projects or curricula?

We are excited to announce our upcoming virtual workshop series for Summer 2023. Our interactive, hands-on workshops are taught by experienced NCBI Education faculty. Events are free to attend, and applications are open to the public; however, each workshop will accept a limited number of participants to facilitate the best possible educational experience. Continue reading “New NCBI Summer Virtual Workshop Series!” →

NCBI’s Remap Tool to Retire in November 2023

As of November 2023, NCBI’s Remap tool will no longer be available. Due to low usage of Remap, a tool that projects annotation data from one coordinate system to another, we are focusing our development efforts on our more popular resources and tools.

We encourage you to check out our newest, easy-to-use visualization tool, the Comparative Genome Viewer (CGV), which displays assembly-assembly whole genome alignments to help you quickly compare eukaryotic genome assemblies and easily identify genomic changes that may be significant to biology and evolution.

Stay up to date

Follow us on Twitter @NCBI and join our mailing list to keep up to date with our visualization tools and other NCBI news.  

Questions?

Feel free to contact our help desk at info@ncbi.nlm.nih.gov if you have any questions or concerns.

Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily

We are excited to introduce a new user-validated feature in the Comparative Genome Viewer (CGV) making it easier for you to analyze inverted regions. You can flip the orientation of one of the aligned chromosomes in the view, so the sequence and gene order is facing the same direction for both assemblies.

What’s new?

When looking at genome alignments in CGV, you may find related sequence regions that are inverted in one assembly relative to another. It may be difficult to tell if gene synteny (order and orientation) is conserved in these inverted segments because the relative gene order is reversed.

Now available! Look for the “flip” button on the left side of either the top or bottom chromosome (Figure 1). 

Clicking on the “flip” button will reverse the direction of the chromosome.
Reverse-orientation alignments will still show up as purple but will have an “un-twisted” style.

Continue reading “Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily” →